NFKB1.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	NFKB1.H12INVIVO.0.PS.A
Gene (human)	NFKB1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Nfkb1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	dGGGAAAdhCCC
GC content	58.04%
Information content (bits; total / per base)	13.284 / 1.107
Data sources	ChIP-Seq + HT-SELEX
Aligned words	863

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	7 (37)	0.951	0.988	0.921	0.979	0.931	0.979	4.661	5.501	550.886	853.036
Mouse	7 (35)	0.786	0.927	0.782	0.91	0.733	0.901	3.806	4.485	94.62	438.066

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.646	0.667	0.563	0.583	0.528	0.546
Non-Methyl HT-SELEX, 2 experiments	best	0.742	0.764	0.607	0.634	0.548	0.575

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.318	1.248	0.482	0.296

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Rel homology region (RHR) factors {6.1} (TFClass)
TF family	NFkappaB-related {6.1.1} (TFClass)
TF subfamily	NFkappaB p50-like {6.1.1.1} (TFClass)
TFClass ID	TFClass: 6.1.1.1.1
HGNC	HGNC:7794
MGI	MGI:97312
EntrezGene (human)	GeneID:4790 (SSTAR profile)
EntrezGene (mouse)	GeneID:18033 (SSTAR profile)
UniProt ID (human)	NFKB1_HUMAN
UniProt ID (mouse)	NFKB1_MOUSE
UniProt AC (human)	P19838 (TFClass)
UniProt AC (mouse)	P25799 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	7 human, 7 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	NFKB1.H12INVIVO.0.PS.A.pcm
PWM	NFKB1.H12INVIVO.0.PS.A.pwm
PFM	NFKB1.H12INVIVO.0.PS.A.pfm
Alignment	NFKB1.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	NFKB1.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	NFKB1.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	NFKB1.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	NFKB1.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	NFKB1.H12INVIVO.0.PS.A_homer_format_0.001.txt NFKB1.H12INVIVO.0.PS.A_homer_format_0.0005.txt NFKB1.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	379.0	67.0	193.0	224.0
02	25.0	13.0	781.0	44.0
03	90.0	3.0	752.0	18.0
04	17.0	6.0	831.0	9.0
05	603.25	10.25	243.25	6.25
06	775.25	15.25	67.25	5.25
07	815.25	0.25	44.25	3.25
08	114.25	113.25	229.25	406.25
09	119.25	275.25	32.25	436.25
10	53.25	775.25	26.25	8.25
11	99.25	743.25	5.25	15.25
12	50.25	742.25	42.25	28.25

PFM

	A	C	G	T
01	0.439	0.078	0.224	0.26
02	0.029	0.015	0.905	0.051
03	0.104	0.003	0.871	0.021
04	0.02	0.007	0.963	0.01
05	0.699	0.012	0.282	0.007
06	0.898	0.018	0.078	0.006
07	0.945	0.0	0.051	0.004
08	0.132	0.131	0.266	0.471
09	0.138	0.319	0.037	0.506
10	0.062	0.898	0.03	0.01
11	0.115	0.861	0.006	0.018
12	0.058	0.86	0.049	0.033

PWM

	A	C	G	T
01	0.56	-1.152	-0.111	0.037
02	-2.098	-2.695	1.281	-1.56
03	-0.864	-3.836	1.243	-2.402
04	-2.454	-3.342	1.343	-3.013
05	1.023	-2.902	0.119	-3.31
06	1.273	-2.552	-1.149	-3.445
07	1.324	-4.719	-1.555	-3.785
08	-0.629	-0.638	0.06	0.629
09	-0.587	0.242	-1.857	0.7
10	-1.376	1.273	-2.052	-3.085
11	-0.767	1.231	-3.445	-2.552
12	-1.432	1.23	-1.599	-1.983

Standard thresholds

P-value	Threshold
0.001	3.71446
0.0005	4.764815
0.0001	6.97402